We developed a novel pre-separation method of trans fatty acids (TFAs) using a silver-ion cartridge column and GC. As a preliminary study, a mixture of fatty acid methyl esters consisting of saturated, cis-unsaturated, and trans-unsaturated fatty acids was dissolved in dichloromethane and loaded onto a Bond Elut SCX ion-exchange cartridge column that was converted to the silver-ion form. The column was then eluted with dichloromethane to obtain the saturated fatty acids, dichloromethane/ethyl acetate (90/10) for the trans mono-ene, dichloromethane/ethyl acetate (65/35) for the cis mono-ene, dichloromethane/acetone (60/40) for the trans di-ene, and acetone/acetonitrile (80/20) for the others. Satisfactory separation of the cis/trans isomers was confirmed by GC analysis. To generalize this technique, the elution conditions of the ready-to-use Discovery Ag-ION SPE cartridge column were also optimized. Both cartridge columns had good separation, recovery, and repeatability. Peer laboratory verification was carried out between two laboratories using different production lots of the ready-to-use cartridge column, and the robustness of the product and reproducibility of the method were found to be satisfactory. This technique is therefore a powerful tool not only for routine analyses of TFAs in oils, fats, and foods but also for detailed analyses of TFAs in various research fields.